FINAL MURPHY STUDY GUIDE

The conversion of Folate to THF requires the addition of electrons from NADH. Which of the below enzymes are inhibited by methotrexate to aid in treatment of acute leukemia?

Dihydrofolate oxidase

THF hydrolase

dihydrofolate reductase

THF reductase

dihydrofolate reductase

Coenzyme vitamin B12 is used in which of the synthesis of which of the following amino acids?

Alanine

Methionine

Tryptophan

Proline

Methionine

One-carbon carriers in metabolism include:

Biotin

Folate (THF)

SAM

All of the above

All of the above

All of the following statements concerning folic acid are true except:

Folic acid requires intrinsic factor for its absorption in the intestine

N5,N10-methylene THF is a product of the cleavage of glycine

Vitamin B12 is required for the N5-methyl THF-dependent conversion of homocysteine to methionine

N10-formyl THF, CO2, and aspartate are precursors in the synthesis of hypoxanthine

Folic acid is a B vitamin

Folic acid requires intrinsic factor for its absorption in the intestine

PLP is a coenzyme used in many reaction types in biochemistry. Which of the following is a reaction that PLP participates in?

Ligations

Decarboxylations

Chlorination reactions

Epimerization reactions

Decarboxylations

Most aminotransferases utilize ________as the recipient alpha-keto acid

alpha-Ketoglutarate

Pyruvate

Oxaloacetate

Phenylpyruvate

Imidazole Pyruvate

alpha-Ketoglutarate

All of the following are purine bases except _____.

Guanine

Thymine

Adenine

Hypoxanthine

All of the above are purines

Thymine

What is the major mechanistic difference in purine and pyrimidine biosynthesis? Purines are much simpler than pyrimidines

Pyrimidines utilize amino acids during synthesis

Purines are synthesized on the ring of ribose

IMP is formed in both pathways

Pyrimidine synthesis is performed before purine

Purines are synthesized on the ring of ribose

All of the following are directly involved in the synthesis of deoxyribonucleic acid except _______.

Thioredoxin

NADPH

Ribonucleotide reductase

Thioredoxin reductase

HGPRT

HGPRT

Long strands of nucleotides are broken down into oligonucleotides during the first step of degradation to be re-utilized by which enzyme?

Exonucleases

ribonucleotide reductases

Endonucleases

DNA polymerases

Endonucleases

During nucleic acid degradation oligonucleotides are further cleaved by exonucleases called phosphodiesterase enzymes. What is the name of the product released from the oligonucleotide strand after the exonuclease reaction is finished?

Nucleoside monophosphate

Nucleotide monophosphate

Nucleoside

Nucleotide

Nucleoside monophosphate

Nucleoside monophosphate molecules use enzymes called _______________ and water to cleave off the phosphate from the nucleoside monophosphate and a final product called a nucleosid

Endonuclease

Nucleoside phosphorylase

Nucleoside kinase

Nucleotidase

Endonuclease

Nucleoside monophosphate molecules use enzymes called _______________ and water to cleave off the phosphate from the nucleoside monophosphate and a final product called a nucleoside

Endonuclease

Nucleoside phosphorylase

Nucleoside kinase

Nucleotidase

Endonuclease

Which of the following is in the proper order of nucleic acid degradation from largest molecule to smallest?

nucleic acid, oligonucleotide, nucleoside, nucleoside monophosphate, nucleobase

nucleic acid, oligonucleotide, nucleoside monophosphate, nucleobase, nucleoside

nucleic acid, oligonucleotide, nucleoside monophosphate, nucleoside, nucleobase

nucleic acid, oligonucleotide , nucleobase, nucleoside monophosphate, nucleoside

nucleic acid, oligonucleotide, nucleoside monophosphate, nucleoside, nucleobase

Ribonucleoside diphosphate reductase (rNDP), is an enzyme that catalyzes the formation of deoxyribonucleotides from ribonucleotides. It catalyzes this formation by removing the 2'-hydroxyl group of the ribose ring of nucleoside diphosphates. There are two different deoxyribonucleoside diphosphates (dNDP) molecules that can be metabolized down the line to deoxy-TTP. Select the pair of dNDP molecules below that can synthesize dTTP.

dCDP and dUDP

dCDP and dADP

dADP and dGDP

dUDP and dGDP

dCDP and dUDP

Ribonucleotide reductase (RNR) reduces all four ribonucleotides. Ribonucleotide reductase (RNR) uses three classes for the free radical needed for the reaction. Class I uses a catalytic Tyr radical. Class II and Class III use two molecules to generate a radical. Pick the proper pair below that are used in Class II and Class III.

S-adenosylmethionine and B12

B12 and THF

THF and S-adenosylmethionine

Tyr and B12

S-adenosylmethionine and B12

Which of the following molecules is the first intermediate made in adenosine catabolism to uric acid?

AMP

Xanthine

Hypoxanthine

Inosine

Inosine

GMP is converted to Guanosine during the catabolism of purines. Guanosine is then converted in one step to which of the following molecules during purine catabolism?

Xanthosine

Xanthine

Guanine

Hypoxanthine

Guanine

The following is the general flow of molecules for all purine catabolism as it flows starting from the monophosphate version to uric acid. Each answer below has the first word on the left starting at the beginning of catabolism (closest to the monophosphate molecules) and then finishing on the right-most word being closest to uric acid

nucleotide --> nucleoside --> nucleobase

nucleotide --> nucleobase --> nucleoside

nucleoside --> nucleotide --> nucleobase

nucleoside --> nucleobase --> nucleotide

nucleotide --> nucleoside --> nucleobase

A phosphate is removed from the monophosphate molecules of AMP, IMP, XMP and/or GMP to form nucleosides. In the next step, the sugar ribose is removed from the nucleoside generating ribose-1-phosphate (ribose-1-P-). Where did this phosphate come from?

There were two phosphate molecules on the original nucleotides

The ribose of the AMP, GMP, IMP, and/or XMP have phosphates on them at their 1 position

The process of removing the phosphate from AMP, GMP, IMP and or XMP places a phosphate onto the ribose at the 1-position

The nucleosides undergo a reaction with purine nucleoside phosphorylase resulting in the release of a phosphorylated ribose

The nucleosides undergo a reaction with purine nucleoside phosphorylase resulting in the release of a phosphorylated ribose

Which of the following statements about hormones are correct?

1. Hormones can be peptides, steroids, or amino acid derivatives.

2. Hormones can stimulate the synthesis of target proteins through the activation of specific genes.

3. Hormones can directly activate or inhibit enzymes through the action of signal molecules. 4. Hormones can increase the cellular uptake of metabolites.

1, 2, 4

1, 2

1, 2, 3

All of the above

None of the above

1, 2, 4

Which of the following statements about insulin is not true?

Insulin is involved in regulating blood glucose levels

Insulin inhibits gluconeogenesis via an allosteric effect on PEP carboxykinase

Insulin binds to receptor tyrosine kinases on the outside of the cell membrane

Diabetes can be caused by desensitization of cells to insulin

Insulin is a water-soluble peptide hormone produced by pancreatic β-cells

Insulin inhibits gluconeogenesis via an allosteric effect on PEP carboxykinase

Which of the following steps results in resetting a G-coupled protein to a state where it can respond to additional ligand binding events in the futur

The slow hydrolysis of GTP to GDP by the alpha subunit

The exchange of GDP to GTP on the alpha subunit by a GEF protein

The binding of a ligand to the transmembrane receptor

The gamma subunit hydrolyzes GTP to GDP

None of the steps are correct

The slow hydrolysis of GTP to GDP by the alpha subunit

What is this a representation of:

The repeating backbone structure of RNA

The repeating backbone structure of proteins

The repeating backbone structure of lipids

The repeating backbone structure of DNA

The repeating backbone structure of carbohydrates

The repeating backbone structure of RNA

The DNA "backbone" is composed of

An amide bond between deoxyribose and a nitrogenous base

A glycosidic bond between deoxyribose and a nitrogenous base

A phosphodiester bond between 3' and 5' hydroxyl groups of adjacent deoxyribose residues

A phosphodiester bond between 2' and 5' hydroxyl groups of adjacent deoxyribose residues

None of the above

A phosphodiester bond between 3' and 5' hydroxyl groups of adjacent deoxyribose residues

Write the flow of genetic information as stated in the central dogma of molecular biology:

DNA → RNA → Proteins

During the DNA polymerase reaction, which of the following aspects of the primer strand is required for the addition of a new nucleotide onto the growing DNA strand?

The 2' OH of the ribose sugar located on the existing DNA strand is required for the addition of a new nucleotide onto the growing DNA strand

The 3' OH of the ribose sugar located on the existing DNA strand is required for the addition of a new nucleotide onto the growing DNA strand

The 2' OH of the ribose sugar located on the nucleotide about to be incorporated is required for the addition of a new nucleotide onto the growing DNA strand

The 3' OH of the ribose sugar located on the nucleotide about to be incorporated is required for the addition of a new nucleotide onto the growing DNA strand

The 3' OH of the ribose sugar located on the existing DNA strand is required for the addition of a new nucleotide onto the growing DNA strand

There are multiple types of DNA polymerase in bacteria that serve different functions. Select which of the following DNA polymerase molecules is responsible for filling in spaces left by excised RNA primers on the lagging strand of DN

DNA polymerase I

DNA polymerase II

DNA polymerase III

DNA polymerase IV

DNA polymerase I

DNA ligase is responsible for sealing the DNA backbone of the DNA lagging strands during DNA replication in eukaryotes. Why does DNA ligase need ATP to perform the mechanism of ligation?

The hydrolysis of ATP is solely necessary for overcoming the energetic barrier of performing DNA ligation

The phosphate group of the ATP is added into the DNA strand that you are ligating

The ribose sugar of the ATP is added into the DNA strand that you are ligating

The ATP supplies the adenylate group that is added onto DNA ligase, which isessential for the ligation reaction

The ATP supplies the adenylate group that is added onto DNA ligase, which isessential for the ligation reaction

Small fragments of DNA called Okazaki fragments are generated on the lagging strand during DNA replication. DNA polymerase would not be able to synthesize any DNA on this strand without which of the following enzymes performing its reaction immediately prior to DNA polymerase incorporating new nucleotides?

DNA polymerase I

Primase

Ligase

Helicase

Single-stranded binding proteins

Primase

The following enzyme utilizes ATP to drive parental strand unwinding during DNA replication:

Helicase

Topoisomerase

DNA polymerase I

Ligase

Primase

Helicase

Reverse Transcriptase is in the lab to create which molecule that enables PCR to be done?

mRNA

cDNA

ssDNA

dsRNA

cDNA

Primers are required for Reverse Transcriptase to perform its role as a DNA polymeras Which of the two types of primers are used in the lab to prime mRNA for Reverse Transcription?

random hexamer primers

short hairpin primers

oligo dT primers

A and B

A and C

A and C

Coli have -10 and -35 promoter sites that are highly conserved in prokaryotic proximal promoters. Which eukaryotic proximal promoter site is the counterpart to the bacterial -10 promoter site?

The TATA box

The CG rich region

The CAAT site

The AP-1 site

5' UTR

The TATA box

DNA Footprinting was used to show what about RNA polymerase in Coli? Footprinting was used to show how the mediator interacted with RNA polymerase

Footprinting was used to identify the transcription factor bound to the distal site

Footprinting showed that RNA polymerase was bound to the -35 and -10 region

Footprinting showed that DNA polymerase was bound to the -35 and -10 region

Footprinting showed that RNA polymerase was bound to the -35 and -10 region

Enhancer regions are distal from the start site by 1,000 or more base pairs. Which of the following is true of enhancer sites?

They are frequently monomeric binding sites that bind multiple types of enhancers

They often are groups directly after one another

They are mostly found in the minor grooves of DNA

They commonly exist as pairs with a space between them

They commonly exist as pairs with a space between them

In promoters (and other regions of DNA) there are sequences which occur most often at a certain positions, but can occasionally be different. These sequences are referred to as?

Consensus sequence

Repeat sequence

Response element

Restriction sites

Consensus sequence

Which of the following is a role of the 7-methylguanosine cap?

It aids is transcription termination

It stabilizes the messenger RNA

Provides energy for translation

Is involved in mRNA splicing

It stabilizes the messenger RNA

Eukaryotic mRNA have a 7-methylguanosine cap applied to their 5' end for which of the following events to occur?

Mitochondrial incorporation

Termination of translation

Nuclear export

Enhancing mRNA degradation

Nuclear export

How is the 7-methylguanosine cap found on eukaryotic mRNA biochemically different from a normal guanosine base incorporation in mRN

The 5' phosphate of the pre-mRNA is bound to the 5' phosphate of the 7-methylguanosine cap

The ribose of the 7-methylguanosine cap is deoxygenated

The 7-methylguanosine cap has seven methyl groups on the guanosine base The 7-methylguanosine cap is added onto the mRNA by DNA polymerase III

The 5' phosphate of the pre-mRNA is bound to the 5' phosphate of the 7-methylguanosine cap

What catalyzes DNA synthesis?

DNA polymerase

Replication fork

Primer

dNTPs

DNA polymerase

Which part of a deoxynucleoside triphosphate (dNTP) molecule provides the energy for DNA synthesis?

Free 3' hydroxyl (-OH) group

Phosphate groups

Base

Sugar

Phosphate groups

Which of the following enzymes is important for relieving the tension in a helix as it unwinds during DNA synthesis?

Topoisomerase

Helicase

Single-stranded binding proteins

Ligase

Topoisomerase

The new DNA strand that grows continuously in the 5' to 3' direction is called the

leading strand

During DNA replication, an open section of DNA, in which a DNA polymerase can replicate DNA, is called a

replication fork

Which of the following statements about hormones are correct?

1. Hormones can be peptides, steroids, or amino acid derivatives.

2. Hormones can stimulate the synthesis of target proteins through the activation of specific genes.

3. Hormones can directly activate or inhibit enzymes through the action of signal molecules.

4. Hormones can increase the cellular uptake of metabolites.

1, 2, 4

Which of the following are characteristics of G protein-coupled receptors (GPCRs)?

1. They typically have seven transmembrane domains that are embedded in the cell membrane.

2. They carry hydrophilic portions of protein that extend into the extracellular matrix as well as the cytosol.

2. The receptor region is located on the extracellular portion of the protein.

4. Most work in concert with G proteins.

All

_____ catalyzes the production of _____, which then opens an ion channel that releases _____ into the cell's cytoplasm.

Adenylyl cyclase ... cyclic AMP ... Ca2+

Protein kinase ... PIP2 ... Na+

Phospholipase C ... IP3 .... Ca2+

Adenylyl cyclase ... IP3 .... Ca2+

Phospholipase C ... cyclic AMP ... Ca2+

Phospholipase C ... IP3 .... Ca2+

The minor groove contains less information about the identity of base pairs than the major groove because of the

geometry of base pairing and structure of ribose.

glycosidic bond angles and structure of pyrimidine bases.

glycosidic bond angles and geometry of base pairings.

glycosidic bond angles and structure of purine bases.

glycosidic bond angles and structure of pyrimidine bases.

Which of the three base pairs has the largest number of hydrogen bonds between the bases?

guanine-cytosine

Jacob and Monod proposed a unified hypothesis of gene regulation. Which of the following statement describes their hypothesis best?

Operons contain regulatory elements that control the expression of contiguous genes.

Repressors and operators regulate messenger RNA

.Transcription is regulated specifically at the level of initiation.

All of the listed statements are part of the hypothesis.

All

Arrange the following events for the synthesis of RNA in the correct order:

Nucleophilic attack of the 3′ OH group of the first nucleotide at the α-phosphate group of the second nucleotide 5′ triphosphate occurs.

Template specific rNTPs are bound.

Several DNA bases are unwound, forming a stable complex.

Polymerase finds a promoter region.

A Mg+2-dependent isomerization of DNA takes place.

4, 3, 5, 2, 1

Which of the following address(es) the problems posed by chromatin during transcription?

In some instances, protein factors can interfere with chromatin structure at specific locations, opening sensitive sites.

In some cases, chromatin structure rearranges at the time of replication.

The action of chromatin remodeling factors is involved, which require ATP hydrolysis to allow the promoter regions to accept the complex.

All of the listed statements are true.

All

Translation occurs in the _____.

cytoplasm

lysosome

nucleus

mitochondrion

nucleoplasm

cytoplasm

Which of the following lists steps of mRNA production in eukaryotes in the correct order?

Transcription, 5' cap addition, addition of poly-A tail, exon splicing, passage through nuclear membrane

Which of the following is characteristic of transcription in eukaryotes but not in prokaryotes?

Exon splicing

A 5' untranslated leader sequence

A single transcript may be transcribed and translated simultaneously

A 3' untranslated trailer sequence

Exon splicing

Which of the following are characteristics of translation?

Each tRNA binds one amino acid and also carries an activating enzyme for this amino acid, known as an amino transferase.

The anticodon region of the tRNA binds to a complementary codon region on mRNA.

mRNA is read in the 3′ to 5′ direction.

The resulting polypeptide is synthesized from its N terminus.

2 and 4

Amino acids are activated by aminoacyl-tRNA synthetases--this incorporates the amino acid to the 3′ terminal end of an invariant adenosine residue on the tRNA. Which of the following statements about this enzyme and the reaction it catalyzes are true?

1. There are a total of 20 aminoacyl-tRNA synthetases (aaRS)--one for each amino acid.

2. The amino acids react with ATP to form a mixed anhydride known as an aminoacyl adenylate.

3. While still bound to the enzyme, a reaction between this anhydride and the free 3′ end of the tRNA occurs.

4. There are two types of aaRS enzymes, each of which has different active sites.

5. In higher eukaryotes, aaRS molecules have acquired additional functionality, such as autoimmunity, control of apoptosis, and regulation for rRNA synthesis.

2, 3, 4, 5

Which of the following events in transcription initiation likely occurs last?

TBP is recruited to the promoter.

Basal transcription factors form a basal transcription complex.

Regulatory transcription factors bind to enhancers.

RNA polymerase binds to the promoter of the gene.

RNA polymerase binds to the promoter of the gene.

What is the function of a spliceosome?

protein activation

translation

protein degradation

regulating the transport of mRNA to the cytoplasm

RNA processing

RNA processing

Nucleosomes are composed of all of the following except ________.

H2B

H3

H2A

H5

H4

H5

The DNA "backbone" is composed of

An amide bond between deoxyribose and a nitrogenous base

A phosphodiester bond between 2' and 5' hydroxyl groups of adjacent deoxyribose residues

None of the above are correct

A glycosidic bond between deoxyribose and a nitrogenous base

A phosphodiester bond between 3' and 5' hydroxyl groups of adjacent deoxyribose residues

A phosphodiester bond between 3' and 5' hydroxyl groups of adjacent deoxyribose residues

Eukaryotic initiation begins with the assembly of ________________.

48S Initiation complex

Translational initiation complex

Preinitiation complex

Poly-binding complex

Cap-binding complex

Preinitiation complex

How many hydrogen bonds exist between this DNA strand and its complimentary strand? TCCAAG

14

22

15

16

15 (Three hydrogen bonds are required to pair C with G and two hydrogen bonds are required to pair T with A)

Which of the following statements is not true of mRNA?

Eukaryotic mRNAs are extensively modified after synthesis

Prokaryotic mRNAs are immediately transmitted into protein without covalent modifications

Eukaryotic mRNAs are mainly monocistronic

Prokaryotic mRNAs are capped with 7-methylguanosine

Prokaryotic mRNAs are mainly polycistronic

Prokaryotic mRNAs are capped with 7-methylguanosine (prokaryotes don't have 5' cap)

The experiment that demonstrated the mechanism whereby DNA is synthesized was performed by

Watson and Crick

Messelson and Stahl

Maurice Wilkins

Linus Pauling

Avery, MacLeod and McCarty

Messelson and Stahl

The classic experiment that demonstrated that radioactively labeled viral DNA transforms bacterial cells was performed by

Hershey and Chase

Griffith

Kossel and Levene

Avery, MacLeod and McCarty

Watson and Crick

Hershey and Chase

In nucleosome structure the histone ___aids in stabilizing the wrapping of DNA around the protein octomer.

H1

H2B

H2A

H3

H4

H1 (linker protein and aid in stablisizing of structure)

DNA molecules are copied or replicated by a _______ mechanism.

Dispersive

All of the above are correct

Semiconservative

Conservative

More than one answer is correct

Semiconservative (parental DNA strands replicate and results in the generation of two daughter chromosomes that contains hybrid of parental chromosome and new DNA strand)

Which of the following describes the flow of genetic information as stated in the central dogma of molecular biology?

RNA --> Protein --> DNA

DNA --> RNA --> Protein

DNA --> Protein --> RNA

Protein --> RNA --> DNA

None of the above are correct

DNA --> RNA --> Protein

Point mutations that occur in a population to any extent are referred to as

Nonsense mutation

Single nucleotide polymorphisms

Missense mutation

Transition mutation

Silent mutations

Single nucleotide polymorphisms

Point mutation with a premature stop signal is referred to as

Nonsense mutation

a point mutation which results into a codon that codes for different amino acid

Missense mutation

a point mutation results in an unmutated codon that codes for same amino acid

Silent mutation

Which of the following is not a second messenger molecule?

Steroids

cGMP

cAMP

Inositol-phospholipid system

Calcium

Steroids

Which of the following does not contribute to the noncovalent interactions that stabilize the helical strands of DNA

Phosphodiester bonds

Hydrogen bonds

Hydrophobic interactions

Hydration

Base stacking

Phosphodiester bonds

Determine the mRNA sequence for the following DNA sequence.5'-GCCATTTCCCGTTA-3'

5'-CGGTAAAGGGCAAT-3'

5'-CGGUAAAGGGCAAU-3'

5'-UAACGGCAAAUGGC-3'

5'-UAACGGGAAAUGGC-3'

5'-TAACGGCAAATGGC-3'

5'-UAACGGGAAAUGGC-3'

prevent protein from folding prematurely (i.e. SecB)

Chaperones

Which of the following describes the flow of genetic information as stated in the central dogma of molecular biology?

DNA to RNA to Protein

Which of the following statements about insulin is not true?

Insulin inhibits gluconeogenesis via an allosteric effect on PEP carboxykinase

Which of the following statements about hormones are correct?

1, 2, and 4 are correct

Which of these is the second of the three stages of cell signaling?

transduction

Under which conditions are the lac structural genes expressed most efficiently?

No glucose, high lactose

Which of the following best describes the role of EF-Tu (elongation factor Tu) in elongation of protein synthesis?

It is involved in the correct binding of amino acyl tRNA to the A site of the ribosome

The DNA "backbone" is composed of

A phosphodiester bond between 3' and 5' hydroxyl groups of adjacent deoxyribose residues

Posttranslational modifications include all except

disulfide bond formation

The process of translation is extremely accurate (1 mistake in 10,000) due to

answers B and C are correct (B: codon/anti-codon interactions. C: amino-acyl tRNA synthetases)

How many hydrogen bonds exist between this DNA strand and its complimentary strand?

TCCAAG

15

Eukaryotic DNA is packaged very differently than bacterial DNA. Which of the following statements is true of eukaryotic DNA packaging?

It is packaged with special proteins known as histones.

Which of the following statements about the ubiquitination of proteins are true?

Only statements 1, 2, and 4 are correct.

A researcher will do which of the following to elucidate how a known receptor mediated, polar protein molecule signals through the cell ultimately changing transcription of genes. Pick the best choice.

Run a transcriptome array to determine all the changes in every gene level in treated vs untreated cells.

The classic experiment that demonstrated that radioactively labeled viral DNA transforms bacterial cells was performed by

Hershey and Chase

Why would siRNA be preferred over a chemical inhibitor that targets the same molecule?

Off targets of chemical inhibition may occur where siRNA is specific to a desired mRNA.

Determine the primary sequence of a protein that would be produced from the following non-coding DNA sequence.

5'-GGCCATTTCCCGTAT-3'

Ile-Arg-Glu-Met-Ala

The following is a hypothetical experimental result obtained after treatment of a cell type with a toxin (Tox) compared to control (control). A western blot was run and the results of the western blot are shown below. Which of the following experiment(s) would most directly show that the increase of protein was due to mRNA stabilization?

A & B

(A: Run real-time PCR on the mRNA of the gene

B: Perform a luciferase assay on the promoter of the gene)

Which of the following is not a second messenger molecule?

Steroids

The intracellular portion of the G-Coupled Protein that exchanges GDP for

GTP, dissociating from the other two and becomes active is called?

alpha

The type of hormone receptors that are found within the cell are called?

Nuclear Receptors

When v-snares and t-snares pull together what is the result of the

membrane and proteins involved?

There is a tension supplied by the t-snares and v-snares that results in

membrane fusion and the subsequent deliver of protein to the extracelluar

space.

Which of the following best describes the role of EF-Tu (elongation factor

Tu) in elongation of protein synthesis?

It is involved in the correct binding of amino acyl tRNA to the A site of the ribosome